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- PDB-6sbj: X-ray structure of mus musculus Fumarylacetoacetate hydrolase dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sbj | |||||||||
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Title | X-ray structure of mus musculus Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) apo-form uuncomplexed | |||||||||
![]() | Acylpyruvase FAHD1, mitochondrial | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / mitochondrion / nucleoplasm ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / mitochondrion / nucleoplasm / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rupp, B. / Naschberger, A. / Weiss, A.K.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse. Authors: Weiss, A.K.H. / Naschberger, A. / Cappuccio, E. / Metzger, C. / Mottes, L. / Holzknecht, M. / von Velsen, J. / Bowler, M.W. / Rupp, B. / Jansen-Durr, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.1 KB | Display | ![]() |
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PDB format | ![]() | 269 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6sbiC ![]() 6fohS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 29412.994 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8R0F8, acylpyruvate hydrolase, oxaloacetate decarboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 27 % / Description: thin needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% (w/v) PEG 3350, 0.2 M MgCl2 and 0.1 M Bis/Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2018 |
Radiation | Monochromator: Diamond C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.217→42.65 Å / Num. obs: 26144 / % possible obs: 89.2 % / Redundancy: 3.44 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.159 / Rrim(I) all: 0.298 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.217→2.466 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1316 / CC1/2: 0.553 / Rpim(I) all: 0.609 / Rrim(I) all: 1.138 / % possible all: 45.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FOH Resolution: 2.22→42.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.521 / SU Rfree Cruickshank DPI: 0.341 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.31 Å2 / Biso mean: 27.656 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 2.22→42.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.22→2.273 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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